FMO DATABASE

FMODB ID: 5J95Z

Calculation Name: 3M5B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M5B

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y2Y4

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-803476.177534
FMO2-HF: Nuclear repulsion	762410.722594
FMO2-HF: Total energy	-41065.45494
FMO2-MP2: Total energy	-41186.874133

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:5:PRO)

Summations of interaction energy for fragment #1(A:5:PRO)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-6.342	0.071	0.79	-2.853	-4.35	-0.01

Interaction energy analysis for fragmet #1(A:5:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.000

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	7	ARG	1	0.995	1.013	3.371	0.286	2.268	0.033	-0.967	-1.048	0.001
4	A	8	LEU	0	-0.031	-0.020	5.295	0.476	0.517	-0.001	-0.004	-0.036	0.000
5	A	9	PRO	0	-0.031	-0.028	8.751	0.046	0.046	0.000	0.000	0.000	0.000
6	A	10	SER	0	0.014	0.013	11.450	0.108	0.108	0.000	0.000	0.000	0.000
7	A	11	PRO	0	-0.039	-0.020	14.202	0.000	0.000	0.000	0.000	0.000	0.000
8	A	12	TYR	0	0.023	-0.010	17.309	0.052	0.052	0.000	0.000	0.000	0.000
9	A	13	GLY	0	0.011	0.007	17.422	0.024	0.024	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.041	-0.015	18.246	0.003	0.003	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.837	-0.900	21.742	-0.195	-0.195	0.000	0.000	0.000	0.000
12	A	16	ARG	1	0.985	0.971	23.856	0.161	0.161	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.035	-0.024	26.118	0.003	0.003	0.000	0.000	0.000	0.000
14	A	18	VAL	0	0.041	0.034	20.704	0.007	0.007	0.000	0.000	0.000	0.000
15	A	19	GLN	0	0.018	0.000	21.019	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	20	LEU	0	-0.078	-0.037	22.582	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.010	0.003	24.138	0.007	0.007	0.000	0.000	0.000	0.000
18	A	22	ALA	0	0.011	0.009	19.309	0.007	0.007	0.000	0.000	0.000	0.000
19	A	23	ARG	1	0.888	0.943	21.202	0.237	0.237	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.049	-0.016	23.072	0.012	0.012	0.000	0.000	0.000	0.000
21	A	25	ARG	1	0.910	0.992	16.545	0.318	0.318	0.000	0.000	0.000	0.000
22	A	26	PRO	0	0.050	0.000	23.675	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.017	0.001	26.069	0.012	0.012	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.027	-0.033	28.548	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	29	CYS	0	-0.090	0.003	26.296	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	30	ASP	-1	-0.771	-0.861	29.006	-0.108	-0.108	0.000	0.000	0.000	0.000
27	A	31	THR	0	-0.017	-0.011	27.350	0.009	0.009	0.000	0.000	0.000	0.000
28	A	32	LEU	0	-0.020	-0.008	26.958	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	33	ILE	0	0.020	0.014	23.710	0.009	0.009	0.000	0.000	0.000	0.000
30	A	34	THR	0	0.005	0.005	24.813	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	35	VAL	0	0.051	0.018	20.668	0.003	0.003	0.000	0.000	0.000	0.000
32	A	36	GLY	0	-0.006	-0.009	23.394	0.007	0.007	0.000	0.000	0.000	0.000
33	A	37	SER	0	-0.031	-0.032	24.997	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	38	GLN	0	-0.018	0.005	18.489	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.913	-0.956	23.699	-0.064	-0.064	0.000	0.000	0.000	0.000
36	A	40	PHE	0	-0.009	-0.009	18.023	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	41	PRO	0	0.000	-0.002	23.110	0.003	0.003	0.000	0.000	0.000	0.000
38	A	42	ALA	0	0.017	0.001	23.309	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	43	HIS	0	0.005	0.012	24.943	0.003	0.003	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.032	-0.040	26.512	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	45	LEU	0	-0.009	-0.014	28.447	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.008	-0.003	22.570	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	47	LEU	0	-0.002	0.001	22.759	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	48	ALA	0	0.020	0.002	24.971	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	49	GLY	0	-0.078	-0.018	26.204	0.005	0.005	0.000	0.000	0.000	0.000
46	A	50	VAL	0	-0.022	-0.004	20.434	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	51	SER	0	-0.021	-0.027	23.701	0.006	0.006	0.000	0.000	0.000	0.000
48	A	52	GLN	0	0.013	0.005	25.592	0.005	0.005	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.016	-0.001	26.720	0.002	0.002	0.000	0.000	0.000	0.000
50	A	54	LEU	0	0.030	0.002	22.209	0.008	0.008	0.000	0.000	0.000	0.000
51	A	55	GLY	0	0.007	0.022	26.796	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	56	ARG	1	0.843	0.937	29.246	0.093	0.093	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.976	0.990	30.291	0.074	0.074	0.000	0.000	0.000	0.000
54	A	58	GLY	0	-0.015	-0.008	32.506	0.006	0.006	0.000	0.000	0.000	0.000
55	A	59	GLN	0	0.010	0.003	30.657	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	60	TRP	0	-0.033	-0.028	25.837	0.007	0.007	0.000	0.000	0.000	0.000
57	A	61	ALA	0	-0.004	0.005	28.166	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	62	LEU	0	0.011	0.006	21.856	0.001	0.001	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.000	-0.018	25.459	0.004	0.004	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.969	-0.980	24.238	-0.043	-0.043	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.004	0.012	23.166	0.004	0.004	0.000	0.000	0.000	0.000
62	A	66	ILE	0	0.004	0.013	18.560	0.004	0.004	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.001	-0.002	16.122	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	68	PRO	0	0.052	0.006	17.813	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	69	SER	0	-0.008	0.002	11.885	-0.056	-0.056	0.000	0.000	0.000	0.000
66	A	70	THR	0	0.031	0.018	13.340	-0.036	-0.036	0.000	0.000	0.000	0.000
67	A	71	PHE	0	0.028	0.003	14.394	-0.053	-0.053	0.000	0.000	0.000	0.000
68	A	72	ALA	0	0.017	0.011	14.364	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	73	GLN	0	-0.015	-0.012	8.771	-0.041	-0.041	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.004	0.009	12.311	-0.067	-0.067	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.015	-0.012	14.963	-0.019	-0.019	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.085	0.039	12.012	0.056	0.056	0.000	0.000	0.000	0.000
73	A	77	PHE	0	-0.003	0.010	11.735	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.037	-0.014	14.071	0.002	0.002	0.000	0.000	0.000	0.000
75	A	79	TYR	0	-0.034	-0.038	17.214	0.033	0.033	0.000	0.000	0.000	0.000
76	A	80	GLY	0	-0.034	-0.013	16.616	0.011	0.011	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.940	-0.968	12.217	-0.575	-0.575	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.042	-0.056	8.743	0.061	0.061	0.000	0.000	0.000	0.000
79	A	83	VAL	0	0.009	0.019	7.124	0.030	0.030	0.000	0.000	0.000	0.000
80	A	84	GLU	-1	-0.944	-0.983	2.437	-5.406	-3.995	0.478	-0.675	-1.214	-0.002
81	A	85	LEU	0	-0.054	-0.008	3.343	0.245	0.736	0.025	-0.132	-0.383	-0.001
82	A	86	GLN	0	0.070	0.017	3.078	-0.650	1.789	0.256	-1.068	-1.628	-0.008
83	A	87	PRO	0	0.030	-0.003	4.534	-0.666	-0.617	-0.001	-0.007	-0.041	0.000
84	A	88	GLY	0	-0.065	-0.037	6.536	-0.337	-0.337	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.831	-0.911	6.760	0.050	0.050	0.000	0.000	0.000	0.000
86	A	90	LEU	0	0.038	0.029	8.324	-0.113	-0.113	0.000	0.000	0.000	0.000
87	A	91	ARG	1	0.903	0.945	10.116	-0.248	-0.248	0.000	0.000	0.000	0.000
88	A	92	PRO	0	0.066	0.033	12.367	-0.030	-0.030	0.000	0.000	0.000	0.000
89	A	93	LEU	0	0.030	0.014	10.147	-0.022	-0.022	0.000	0.000	0.000	0.000
90	A	94	GLN	0	0.005	-0.003	13.909	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	95	GLU	-1	-0.985	-0.993	15.816	0.039	0.039	0.000	0.000	0.000	0.000
92	A	96	ALA	0	0.016	0.017	16.835	0.000	0.000	0.000	0.000	0.000	0.000
93	A	97	ALA	0	-0.018	-0.025	16.742	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	98	ARG	1	0.946	0.981	18.649	0.055	0.055	0.000	0.000	0.000	0.000
95	A	99	ALA	0	-0.026	0.000	21.536	0.003	0.003	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.011	-0.007	20.506	0.003	0.003	0.000	0.000	0.000	0.000
97	A	101	GLY	0	0.052	0.038	23.401	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.017	-0.001	18.365	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	103	GLN	0	0.048	0.010	19.293	-0.024	-0.024	0.000	0.000	0.000	0.000
100	A	104	SER	0	0.021	0.001	17.862	0.000	0.000	0.000	0.000	0.000	0.000
101	A	105	LEU	0	-0.032	-0.009	12.347	-0.039	-0.039	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.875	-0.946	14.954	-0.154	-0.154	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.892	-0.957	16.644	-0.212	-0.212	0.000	0.000	0.000	0.000
104	A	108	ALA	0	-0.035	-0.019	12.458	-0.015	-0.015	0.000	0.000	0.000	0.000
105	A	109	CYS	0	-0.038	-0.018	11.823	-0.075	-0.075	0.000	0.000	0.000	0.000
106	A	110	TRP	0	-0.036	-0.013	12.572	0.040	0.040	0.000	0.000	0.000	0.000
107	A	111	ARG	1	0.937	0.966	14.208	0.402	0.402	0.000	0.000	0.000	0.000
108	A	112	ALA	0	-0.045	-0.004	8.766	0.009	0.009	0.000	0.000	0.000	0.000
109	A	113	ARG	1	0.914	0.979	9.980	0.097	0.097	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:PRO)